RNA-seq analysis of tomato genotypes resistant to bacterial spot (Xanthomonas perforans) race T4

Bacterial spot (BS) is one of the most devastating foliar bacterial diseases of tomato and is caused by multiple species of Xanthomonas. We performed RNA sequencing (RNA-seq) analysis of three tomato lines with different levels of resistance to Xanthomonas perforans race T4 to study differentially expressed genes (DEGs) and transcript-based sequence variations. Analysis between inoculated and control samples revealed that the resistant Solanum pimpinellifolium accession PI 270443 had the most DEGs (834), followed by the susceptible genotype tomato (S. lycopersicum L) breeding line NC 714 (373), and intermediate resistant genotype tomato breeding line NC 1CELBR (154). Gene ontology (GO) terms revealed that more GO terms (51) were enriched for upregulated DEGs in the resistant genotype PI 270443, and more downregulated DEGs (67) were enriched in the susceptible genotype NC 714. DEGs in the biotic stress pathway showed more upregulated biotic stress pathway DEGs (67) for PI 270443 compared with more downregulated DEGs (125) for the susceptible NC 714 genotype. Resistant genotype PI 270443 has three upregulated DEGs for pathogenesis-related (PR) proteins, and susceptible genotype NC 714 has one downregulated R gene. Sequence variations called from RNA-seq reads against the reference genome of susceptible ‘Heinz 1706’ showed that chr11, which has multiple reported resistance quantitative trait loci (QTLs) to BS race T4, is identical between the two resistant lines, PI 270443 and NC 1CELBR, suggesting that these two lines share the same resistance QTLs on this chromosome. Several loci for PR resistance proteins with sequence variation between the resistant and susceptible tomato lines were near the known Rx4 resistance gene on chromosome 11, and additional biotic stress-associated DEGs near to the known Rx4 resistance gene were also identified in the susceptible NC 714 line.